On the Lookout

Whole Genome Sequencing (WGS) is a laboratory process that maps out the entire RNA or DNA sequence of an organism. When a pathogen infects a new host and replicates by copying their RNA/DNA, they make small errors that result in mutations. Most of the time these mutations are insignificant, or even detrimental to the pathogen. Rarely, they are advantageous to the pathogen, becoming more easily transmissible, resistant to antibiotics, or better able to evade our immune system. By looking at these mutations, scientists can show how closely related pathogens are to each other and trace disease transmission in real time. WGS helps doctors with treatment decisions by identifying genetic markers that indicate resistance to specific antibiotics. Public health professionals at the federal, state, and local level use these lab reports to enhance disease surveillance and outbreak response. 

Whole genome sequencing has been particularly helpful in responding to food-borne disease outbreaks. Similar to the way DNA left behind at a crime scene can help detectives identify a subject or victim, the RNA/DNA of pathogens is a clue that allow public health to “fingerprint” the cause of outbreaks. For example, if a patient in Oregon tests positive for salmonella, and the stool specimen they provide is cultured, laboratory scientists can determine what exact strain the person contracted. If there are matches with other patients with similar onset dates, this can provide clues to the infection source. If salmonella is identified in a food or environmental sample collected by public health and it matches the salmonella strain from sick patients, then a reliable link can be made. Public health then has the information necessary to take actions like recalling contaminated products, closing a restaurant or factory, or recommending cleaning and disinfecting. Below is a list of the different salmonella strains sequenced in our region of southwest Oregon in 2025. From WGS data we identified one local salmonella outbreak and two cases that were related to larger multi-state clusters.